RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13373
(525 letters)
>gnl|CDD|238386 cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like
enzymes involved in molybdopterin and thiamine
biosynthesis family. The common reaction mechanism
catalyzed by MoeB and ThiF, like other E1 enzymes,
begins with a nucleophilic attack of the C-terminal
carboxylate of MoaD and ThiS, respectively, on the
alpha-phosphate of an ATP molecule bound at the active
site of the activating enzymes, leading to the formation
of a high-energy acyladenylate intermediate and
subsequently to the formation of a thiocarboxylate at
the C termini of MoaD and ThiS. MoeB, as the MPT
synthase (MoaE/MoaD complex) sulfurase, is involved in
the biosynthesis of the molybdenum cofactor, a
derivative of the tricyclic pterin, molybdopterin (MPT).
ThiF catalyzes the adenylation of ThiS, as part of the
biosynthesis pathway of thiamin pyrophosphate (vitamin
B1). .
Length = 228
Score = 338 bits (870), Expect = e-115
Identities = 123/229 (53%), Positives = 162/229 (70%), Gaps = 3/229 (1%)
Query: 132 RYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSN 191
RYSRQILL ++G GQEKL NA VL+VG GG GSP +YLAA+GVG LGL D D VELSN
Sbjct: 1 RYSRQILLPEIGEEGQEKLKNARVLVVGAGGLGSPAAEYLAAAGVGKLGLVDDDVVELSN 60
Query: 192 LHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACD 251
L RQ++HT +GQPK +A + AIN + + AY LD NA ++I YD+V+D D
Sbjct: 61 LQRQILHTEADVGQPKAEAAAERLRAINPDVEIEAYNERLDAENAEELIAGYDLVLDCTD 120
Query: 252 NAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGGPCYRCIYPVPPPAETVGTCGD 311
N TRYL+NDAC++ G+PLVS + LG EGQ+ V+ GPCYRC++P PPP V +C +
Sbjct: 121 NFATRYLINDACVKLGKPLVSGAVLGFEGQVTVFIPGEGPCYRCLFPEPPPPG-VPSCAE 179
Query: 312 NGVLGPVPGVMGTLQAVETIKLL--IGLPVMDKLLVYDAELSKFLSVKL 358
GVLGP+ GV+G+LQA+E +K+L IG P+ +LL++DA F ++KL
Sbjct: 180 AGVLGPLVGVIGSLQALEALKILLGIGEPLAGRLLLFDALSMSFRTLKL 228
>gnl|CDD|236337 PRK08762, PRK08762, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 376
Score = 315 bits (809), Expect = e-103
Identities = 121/261 (46%), Positives = 166/261 (63%), Gaps = 7/261 (2%)
Query: 131 ERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELS 190
ERYSR + L +VG GQ +LL A VL++G GG GSP YLAA+GVGTLG+ D+D V+ S
Sbjct: 114 ERYSRHLRLPEVGEEGQRRLLEARVLLIGAGGLGSPAALYLAAAGVGTLGIVDHDVVDRS 173
Query: 191 NLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDAC 250
NL RQ++HT +GQPKV SA + ++A+N + V A Q + + N +++ DVVVD
Sbjct: 174 NLQRQILHTEDRVGQPKVDSAAQRLAALNPDVQVEAVQERVTSDNVEALLQDVDVVVDGA 233
Query: 251 DNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYN----YKGGPCYRCIYPVPPPAETV 306
DN PTRYLLNDAC++ G+PLV + EGQ+ V++ PCYRC++P PPP E
Sbjct: 234 DNFPTRYLLNDACVKLGKPLVYGAVFRFEGQVSVFDAGRQRGQAPCYRCLFPEPPPPELA 293
Query: 307 GTCGDNGVLGPVPGVMGTLQAVETIKLLIGL--PVMDKLLVYDAELSKFLSVKLRKKKED 364
+C + GVLG +PGV+G LQA E IKLL+G+ P+ +LL +DA +F ++L
Sbjct: 294 PSCAEAGVLGVLPGVIGLLQATEAIKLLLGIGDPLTGRLLTFDALAMRFRELRLPPDPHC 353
Query: 365 CVCA-HPADTQLVDYEVFCSS 384
VCA +DY FC+
Sbjct: 354 PVCAPGRPFPGYIDYAAFCAG 374
>gnl|CDD|180967 PRK07411, PRK07411, hypothetical protein; Validated.
Length = 390
Score = 305 bits (783), Expect = 1e-99
Identities = 159/407 (39%), Positives = 230/407 (56%), Gaps = 31/407 (7%)
Query: 124 KFSKDITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLAD 183
+ SKD ERYSR ++L +VG+ GQ++L ASVL +G GG GSP + YLAA+G+G +G+ D
Sbjct: 10 QLSKDEYERYSRHLILPEVGLEGQKRLKAASVLCIGTGGLGSPLLLYLAAAGIGRIGIVD 69
Query: 184 YDRVELSNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRY 243
+D V+ SNL RQVIH T +G+PK+ SAK I IN V Y+T L + NA DI+ Y
Sbjct: 70 FDVVDSSNLQRQVIHGTSWVGKPKIESAKNRILEINPYCQVDLYETRLSSENALDILAPY 129
Query: 244 DVVVDACDNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGGPCYRCIYPVPPPA 303
DVVVD DN PTRYL+NDAC+ +P V S EGQ V+NY+GGP YR +YP PPP
Sbjct: 130 DVVVDGTDNFPTRYLVNDACVLLNKPNVYGSIFRFEGQATVFNYEGGPNYRDLYPEPPPP 189
Query: 304 ETVGTCGDNGVLGPVPGVMGTLQAVETIKLLIGLP--VMDKLLVYDAELSKFLSVKLRKK 361
V +C + GVLG +PG++G +QA ETIK+++G + +LL+Y+A KF +KLR
Sbjct: 190 GMVPSCAEGGVLGILPGIIGVIQATETIKIILGAGNTLSGRLLLYNALDMKFRELKLRPN 249
Query: 362 KEDCVCAHPADTQLVDYEVFC---SSRANDKTPDISILDPTEHLTALDYRDEFLARRVAH 418
E P +L+DYE FC ++A + I +T + + +
Sbjct: 250 PE-----RPVIEKLIDYEQFCGIPQAKAAEAAQKAEI----PEMTVTELKALLDSGADDF 300
Query: 419 TLLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVICRR 478
L+DVR+ +E+ + + + + D+ E G +E ++E + HR + C+
Sbjct: 301 VLIDVRNPNEYEIARIPGSVLVPLPDI-----ENGPG---VEKVKELLNGHR-LIAHCKM 351
Query: 479 GNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQKYVDNRIPTY 525
G S K + +LK G+ N+K G W + VD +P Y
Sbjct: 352 GGRSAKALGILK------EAGIEG--TNVKGGITAWSREVDPSVPQY 390
>gnl|CDD|180204 PRK05690, PRK05690, molybdopterin biosynthesis protein MoeB;
Provisional.
Length = 245
Score = 295 bits (758), Expect = 8e-98
Identities = 108/242 (44%), Positives = 146/242 (60%), Gaps = 5/242 (2%)
Query: 124 KFSKDITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLAD 183
+ S + RY+RQI+L GQEKL A VL+VG GG G QYLAA+GVGTL L D
Sbjct: 4 ELSDEEMLRYNRQIILRGFDFDGQEKLKAARVLVVGLGGLGCAASQYLAAAGVGTLTLVD 63
Query: 184 YDRVELSNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRY 243
+D V LSNL RQV+H TIGQPKV SA+ ++ IN + + LD +I +
Sbjct: 64 FDTVSLSNLQRQVLHDDATIGQPKVESARAALARINPHIAIETINARLDDDELAALIAGH 123
Query: 244 DVVVDACDNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNY-KGGPCYRCIYPVPPP 302
D+V+D DN TR LN AC +PLVS +A+ +EGQ+ V+ Y PCYRC+ +
Sbjct: 124 DLVLDCTDNVATRNQLNRACFAAKKPLVSGAAIRMEGQVTVFTYQDDEPCYRCLSRLFGE 183
Query: 303 AETVGTCGDNGVLGPVPGVMGTLQAVETIKLL--IGLPVMDKLLVYDAELSKFLSVKLRK 360
TC + GV+ P+ GV+G+LQA+E IKLL G P+ +LL+YDA +F +KL++
Sbjct: 184 NAL--TCVEAGVMAPLVGVIGSLQAMEAIKLLTGYGEPLSGRLLLYDAMTMQFREMKLKR 241
Query: 361 KK 362
Sbjct: 242 DP 243
>gnl|CDD|223552 COG0476, ThiF, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 2
[Coenzyme metabolism].
Length = 254
Score = 270 bits (691), Expect = 1e-87
Identities = 119/244 (48%), Positives = 162/244 (66%), Gaps = 7/244 (2%)
Query: 131 ERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELS 190
ERYSRQILL +G GQ+KL ++ VL+VG GG GSP +YLA +GVG L + D+D VELS
Sbjct: 9 ERYSRQILLPGIGGEGQQKLKDSRVLVVGAGGLGSPAAKYLALAGVGKLTIVDFDTVELS 68
Query: 191 NLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDAC 250
NL RQ + T +G+PK A + + +N V AY LD NA ++I ++DVV+D
Sbjct: 69 NLQRQFLFTEADVGKPKAEVAAKALRKLNPLVEVVAYLERLDEENAEELIAQFDVVLDCT 128
Query: 251 DNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNY-KGGPCYRCIYPVPPPAETVGT- 308
DN TRYL+NDAC++ G PLV A+G EGQ+ V PCYRC++P PP V T
Sbjct: 129 DNFETRYLINDACVKLGIPLVHGGAIGFEGQVTVIIPGDKTPCYRCLFPEKPPPGLVPTS 188
Query: 309 CGDNGVLGPVPGVMGTLQAVETIKLLIG---LPVMDKLLVYDA-ELSKFLSVKLRKKKED 364
C + GVLGP+ GV+G+LQA+E IKLL G P++ +LL+YDA ++ +F ++KLR++
Sbjct: 189 CDEAGVLGPLVGVVGSLQALEAIKLLTGIGLEPLIGRLLLYDALDMERFRTLKLRRRPIS 248
Query: 365 C-VC 367
C VC
Sbjct: 249 CPVC 252
>gnl|CDD|162820 TIGR02356, adenyl_thiF, thiazole biosynthesis adenylyltransferase
ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF
family of proteins (pfam00899) include a number of
members encoded in the midst of thiamine biosynthetic
operons. This mix of known and putative ThiF proteins
shows a deep split in phylogenetic trees, with the
Escherichia. coli ThiF and the E. coli MoeB proteins
seemingly more closely related than E. coli ThiF and
Campylobacter (for example) ThiF. This model represents
the more widely distributed clade of ThiF proteins such
found in E. coli [Biosynthesis of cofactors, prosthetic
groups, and carriers, Thiamine].
Length = 202
Score = 260 bits (666), Expect = 1e-84
Identities = 95/204 (46%), Positives = 135/204 (66%), Gaps = 3/204 (1%)
Query: 132 RYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSN 191
RY+RQ+LL +G GQ++LLN+ VLI+G GG GSP YLA +GVGT+ + D D V+LSN
Sbjct: 1 RYARQLLLPDIGEEGQQRLLNSHVLIIGAGGLGSPAALYLAGAGVGTIVIVDDDHVDLSN 60
Query: 192 LHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACD 251
L RQ++ T +G+PKV A + + +N + V A + + N +I D+V+D D
Sbjct: 61 LQRQILFTEEDVGRPKVEVAAQRLRELNSDIQVTALKERVTAENLELLINNVDLVLDCTD 120
Query: 252 NAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKG-GPCYRCIYPVPPPAETVGTCG 310
N TRYL+NDAC+ G PL+SA+ +G GQL V++ G GPC RC++P +T +C
Sbjct: 121 NFATRYLINDACVALGTPLISAAVVGFGGQLMVFDPGGEGPCLRCLFPDIA--DTGPSCA 178
Query: 311 DNGVLGPVPGVMGTLQAVETIKLL 334
GV+GPV GV+G+LQA+E +KLL
Sbjct: 179 TAGVIGPVVGVIGSLQALEALKLL 202
>gnl|CDD|181156 PRK07878, PRK07878, molybdopterin biosynthesis-like protein MoeZ;
Validated.
Length = 392
Score = 263 bits (673), Expect = 4e-83
Identities = 144/409 (35%), Positives = 214/409 (52%), Gaps = 41/409 (10%)
Query: 126 SKDITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYD 185
++D RYSR +++ VGV GQ++L NA VL++G GG GSP + YLAA+GVGTLG+ ++D
Sbjct: 16 TRDEVARYSRHLIIPDVGVDGQKRLKNARVLVIGAGGLGSPTLLYLAAAGVGTLGIVEFD 75
Query: 186 RVELSNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDV 245
V+ SNL RQVIH +G+ K SA+ I IN V ++ LD SNA ++ +YD+
Sbjct: 76 VVDESNLQRQVIHGQSDVGRSKAQSARDSIVEINPLVNVRLHEFRLDPSNAVELFSQYDL 135
Query: 246 VVDACDNAPTRYLLNDACLREGRPLVSASALGLEGQLCVY----NYKGGPCYRCIYPVPP 301
++D DN TRYL+NDA + G+P V S EGQ V+ G YR +YP PP
Sbjct: 136 ILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGLNYRDLYPEPP 195
Query: 302 PAETVGTCGDNGVLGPVPGVMGTLQAVETIKLL--IGLPVMDKLLVYDAELSKFLSVKLR 359
P V +C + GVLG + +G++ E IKL+ IG P++ +L+VYDA + ++K+R
Sbjct: 196 PPGMVPSCAEGGVLGVLCASIGSIMGTEAIKLITGIGEPLLGRLMVYDALEMTYRTIKIR 255
Query: 360 KKKEDCVCAHPADTQLVDYEVFC---SSRANDKTPDISILDPTEHLTALDYRDEFLARRV 416
K P T+L+DYE FC S A S + P E LD +
Sbjct: 256 KDPST-----PKITELIDYEAFCGVVSDEAQQAAAG-STITPRELKEWLDSGKKIA---- 305
Query: 417 AHTLLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVIC 476
L+DVR E+ ++ + A +++ +GE L L +D R + + C
Sbjct: 306 ---LIDVREPVEWDIVHIPGAQLIPKSEI-----LSGEA---LAKLPQD----RTIVLYC 350
Query: 477 RRGNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQKYVDNRIPTY 525
+ G S + + LK+ D +++ G W K VD +P Y
Sbjct: 351 KTGVRSAEALAALKK-------AGFSDAVHLQGGVVAWAKQVDPSLPMY 392
>gnl|CDD|235526 PRK05597, PRK05597, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 355
Score = 224 bits (573), Expect = 9e-69
Identities = 132/386 (34%), Positives = 190/386 (49%), Gaps = 42/386 (10%)
Query: 132 RYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSN 191
RY RQI+L ++G GQ+ L +A V ++G GG GSP + YLA +GVG + + D D V+LSN
Sbjct: 8 RYRRQIMLGEIGQQGQQSLFDAKVAVIGAGGLGSPALLYLAGAGVGHITIIDDDTVDLSN 67
Query: 192 LHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACD 251
LHRQVIH+T +GQPK SA+ + A+N + V L SNA D +R DV++D D
Sbjct: 68 LHRQVIHSTAGVGQPKAESAREAMLALNPDVKVTVSVRRLTWSNALDELRDADVILDGSD 127
Query: 252 NAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGGPCYRCIYPVPPPAETVGTCGD 311
N TR+L + A R G P V AS LG + QL V++ GP Y ++P PPP +V +C
Sbjct: 128 NFDTRHLASWAAARLGIPHVWASILGFDAQLSVFHAGHGPIYEDLFPTPPPPGSVPSCSQ 187
Query: 312 NGVLGPVPGVMGTLQAVETIKLL--IGLPVMDKLLVYDAELSKFLSVKLRKKKEDCVCAH 369
GVLGPV GV+G+ A+E +KL+ +G P++ KL YD+ + + V +
Sbjct: 188 AGVLGPVVGVVGSAMAMEALKLITGVGTPLIGKLGYYDSLDGTWEYIP--------VVGN 239
Query: 370 PADTQLVDYEVFCSSRANDKTPDISILDPTEHLTALDYRDEFLARRVAHTLLDVRSVDEF 429
PA + V E L A TL+DVR EF
Sbjct: 240 PAVLERVR---------GSTPVHGISGGFGEVLDVPRVS----ALPDGVTLIDVREPSEF 286
Query: 430 AMMSLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVICRRGNDSQKVVQLL 489
A S+ A + ++ + G P + + E V V C G S + V +L
Sbjct: 287 AAYSIPGAHNVPLSAI-----REGANPPSVSAGDE-------VVVYCAAGVRSAQAVAIL 334
Query: 490 KRYVERHRPGVVYDIRNIKEGYKGWQ 515
+R + ++ G +GW
Sbjct: 335 ER-------AGYTGMSSLDGGIEGWL 353
>gnl|CDD|131408 TIGR02355, moeB, molybdopterin synthase sulfurylase MoeB. This
model describes the molybdopterin biosynthesis protein
MoeB in E. coli and related species. The enzyme
covalently modifies the molybdopterin synthase MoaD by
sulfurylation. This enzyme is closely related to ThiF, a
thiamine biosynthesis enzyme that modifies ThiS by an
analogous adenylation. Both MoeB and ThiF belong to the
HesA/MoeB/ThiF family (pfam00899) [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Molybdopterin].
Length = 240
Score = 211 bits (540), Expect = 2e-65
Identities = 108/239 (45%), Positives = 143/239 (59%), Gaps = 5/239 (2%)
Query: 132 RYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSN 191
RY+RQI+L GQE L + VLIVG GG G QYLAA+GVG L L D+D V LSN
Sbjct: 4 RYNRQIILRGFDFDGQEALKASRVLIVGLGGLGCAASQYLAAAGVGNLTLLDFDTVSLSN 63
Query: 192 LHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACD 251
L RQV+H+ IGQPKV SAK ++ IN + ++ LD + +I +D+VVD D
Sbjct: 64 LQRQVLHSDANIGQPKVESAKDALTQINPHIAINPINAKLDDAELAALIAEHDIVVDCTD 123
Query: 252 NAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGG-PCYRCIYPVPPPAETVGTCG 310
N R LN C PLVS +A+ +EGQ+ V+ Y+ G PCYRC+ + E +C
Sbjct: 124 NVEVRNQLNRQCFAAKVPLVSGAAIRMEGQVSVFTYQDGEPCYRCLSRL--FGENALSCV 181
Query: 311 DNGVLGPVPGVMGTLQAVETIKLL--IGLPVMDKLLVYDAELSKFLSVKLRKKKEDCVC 367
+ GV+ PV GV+G+LQA+E IK+L IG P+ K+L+ DA F +KL K VC
Sbjct: 182 EAGVMAPVVGVVGSLQAMEAIKVLAGIGKPLSGKILMIDAMTMSFREMKLPKNPTCPVC 240
>gnl|CDD|216180 pfam00899, ThiF, ThiF family. This family contains a repeated
domain in ubiquitin activating enzyme E1 and members of
the bacterial ThiF/MoeB/HesA family.
Length = 134
Score = 182 bits (464), Expect = 1e-55
Identities = 68/134 (50%), Positives = 90/134 (67%)
Query: 152 NASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSA 211
++ VL+VG GG GSP +YLA +GVG L L D+D VELSNL+RQ++ T IG+PK A
Sbjct: 1 SSRVLVVGAGGLGSPAAEYLARAGVGKLTLVDFDTVELSNLNRQILFTESDIGKPKAEVA 60
Query: 212 KRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACLREGRPLV 271
K + AIN + V AY L N ++++ D+VVDA DN RYLLNDAC++ G PL+
Sbjct: 61 KERLRAINPDVEVEAYPERLTPENLEELLKGVDLVVDALDNFAARYLLNDACVKRGIPLI 120
Query: 272 SASALGLEGQLCVY 285
SA ALG +GQ+ V
Sbjct: 121 SAGALGFDGQVTVI 134
>gnl|CDD|169382 PRK08328, PRK08328, hypothetical protein; Provisional.
Length = 231
Score = 159 bits (405), Expect = 8e-46
Identities = 91/231 (39%), Positives = 129/231 (55%), Gaps = 10/231 (4%)
Query: 131 ERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELS 190
ERY RQI++ GV GQEKL A V +VG GG GSP YLAA+GVG + L D ELS
Sbjct: 8 ERYDRQIMI--FGVEGQEKLKKAKVAVVGVGGLGSPVAYYLAAAGVGRILLIDEQTPELS 65
Query: 191 NLHRQVIHTTHTIGQ-PKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDA 249
NL+RQ++H +G+ PK SAK + N + + + L N ++++ DV+VD
Sbjct: 66 NLNRQILHWEEDLGKNPKPLSAKWKLERFNSDIKIETFVGRLSEENIDEVLKGVDVIVDC 125
Query: 250 CDNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGGPCYRCIYPVPPPAETVGTC 309
DN TRYLL+D ++G PLV + G GQ+ R I+P +
Sbjct: 126 LDNFETRYLLDDYAHKKGIPLVHGAVEGTYGQVTTIVPGKTKRLREIFPKVKKKK----- 180
Query: 310 GDNGVLGPVPGVMGTLQAVETIKLLIGL--PVMDKLLVYDAELSKFLSVKL 358
G +LG GV+G++QA+E IKL+ G P+++KLL+ D + F V+L
Sbjct: 181 GKFPILGATAGVIGSIQAMEVIKLITGYGEPLLNKLLIVDLANNVFEVVEL 231
>gnl|CDD|235528 PRK05600, PRK05600, thiamine biosynthesis protein ThiF; Validated.
Length = 370
Score = 163 bits (415), Expect = 1e-45
Identities = 85/230 (36%), Positives = 126/230 (54%), Gaps = 5/230 (2%)
Query: 131 ERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELS 190
R +RQ+ L G+ QE+L NA VL++G GG G P +Q LA++GVGT+ L D D V++S
Sbjct: 20 RRTARQLALPGFGIEQQERLHNARVLVIGAGGLGCPAMQSLASAGVGTITLIDDDTVDVS 79
Query: 191 NLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDAC 250
N+HRQ++ +G+PKV A + I + V+A + L NA +++ D+V+D
Sbjct: 80 NIHRQILFGASDVGRPKVEVAAERLKEIQPDIRVNALRERLTAENAVELLNGVDLVLDGS 139
Query: 251 DNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYN---YKGGPCYRCIYPVPPPAETVG 307
D+ T++L+ DA G PLV + L G+L V+N G R ++P P +++
Sbjct: 140 DSFATKFLVADAAEITGTPLVWGTVLRFHGELAVFNSGPDHRGVGLRDLFPEQPSGDSIP 199
Query: 308 TCGDNGVLGPVPGVMGTLQAVETIKLL--IGLPVMDKLLVYDAELSKFLS 355
C GVLG V+G L A E IK L IG +L YDA + S
Sbjct: 200 DCATAGVLGATTAVIGALMATEAIKFLTGIGDVQPGTVLSYDALTATTRS 249
>gnl|CDD|238760 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1)
of the ubiquitin-like proteins. This family includes
classical ubiquitin-activating enzymes E1,
ubiquitin-like (ubl) activating enzymes and other
mechanistic homologes, like MoeB, Thif1 and others. The
common reaction mechanism catalyzed by MoeB, ThiF and
the E1 enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of MoaD, ThiS and ubiquitin,
respectively, on the alpha-phosphate of an ATP molecule
bound at the active site of the activating enzymes,
leading to the formation of a high-energy acyladenylate
intermediate and subsequently to the formation of a
thiocarboxylate at the C termini of MoaD and ThiS.
Length = 143
Score = 135 bits (341), Expect = 1e-37
Identities = 55/130 (42%), Positives = 71/130 (54%)
Query: 155 VLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAKRF 214
VL+VG GG GS LA SGVG + L D+D VELSNL+RQ + IG+PK A R
Sbjct: 2 VLLVGLGGLGSEIALNLARSGVGKITLIDFDTVELSNLNRQFLARQADIGKPKAEVAARR 61
Query: 215 ISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACLREGRPLVSAS 274
++ +N V A + N D + D+V+DA DN R LN AC G P++ A
Sbjct: 62 LNELNPGVNVTAVPEGISEDNLDDFLDGVDLVIDAIDNIAVRRALNRACKELGIPVIDAG 121
Query: 275 ALGLEGQLCV 284
LGL G + V
Sbjct: 122 GLGLGGDIQV 131
>gnl|CDD|181084 PRK07688, PRK07688, thiamine/molybdopterin biosynthesis
ThiF/MoeB-like protein; Validated.
Length = 339
Score = 140 bits (355), Expect = 2e-37
Identities = 76/241 (31%), Positives = 124/241 (51%), Gaps = 7/241 (2%)
Query: 130 TERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVEL 189
ERYSRQ L +G GQ+KL VLI+G G G+ + L +GVG + + D D VE
Sbjct: 2 NERYSRQELFSPIGEEGQQKLREKHVLIIGAGALGTANAEMLVRAGVGKVTIVDRDYVEW 61
Query: 190 SNLHRQVIHTTHTIGQ--PKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVV 247
SNL RQ ++T + PK +AK+ + IN + V A + +++ D+++
Sbjct: 62 SNLQRQQLYTESDVKNNLPKAVAAKKRLEEINSDVRVEAIVQDVTAEELEELVTGVDLII 121
Query: 248 DACDNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGGPCYRCIYPVPPPAETVG 307
DA DN TR+++NDA + G P + + +G G PC RC+ P
Sbjct: 122 DATDNFETRFIVNDAAQKYGIPWIYGACVGSYGLSYTIIPGKTPCLRCLLQSIP--LGGA 179
Query: 308 TCGDNGVLGPVPGVMGTLQAVETIKLLIGLP--VMDKLLVYDAELSKFLSVKLRK-KKED 364
TC G++ P ++ + Q E +KLL+G + D L+ +D +++ + ++K KK++
Sbjct: 180 TCDTAGIISPAVQIVASYQVTEALKLLVGDYEALRDGLVSFDVWKNEYSCMNVQKLKKDN 239
Query: 365 C 365
C
Sbjct: 240 C 240
>gnl|CDD|183547 PRK12475, PRK12475, thiamine/molybdopterin biosynthesis MoeB-like
protein; Provisional.
Length = 338
Score = 138 bits (349), Expect = 1e-36
Identities = 77/244 (31%), Positives = 121/244 (49%), Gaps = 11/244 (4%)
Query: 129 ITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVE 188
+ ERYSRQIL +G GQ K+ VLIVG G G+ + L +G+G L +AD D VE
Sbjct: 1 MQERYSRQILFSGIGEEGQRKIREKHVLIVGAGALGAANAEALVRAGIGKLTIADRDYVE 60
Query: 189 LSNLHRQVIHTTHTIGQ--PKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVV 246
SNL RQ ++T Q PK +AK + IN + T + ++++ D++
Sbjct: 61 WSNLQRQQLYTEEDAKQKKPKAIAAKEHLRKINSEVEIVPVVTDVTVEELEELVKEVDLI 120
Query: 247 VDACDNAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGGPCYRCIYPVPPPAETV 306
+DA DN TR L+ND + P + +G G PC RC+ P V
Sbjct: 121 IDATDNFDTRLLINDLSQKYNIPWIYGGCVGSYGVTYTIIPGKTPCLRCLMEHVP----V 176
Query: 307 G--TCGDNGVLGPVPGVMGTLQAVETIKLLIG--LPVMDKLLVYDAELSKFLSVKL-RKK 361
G TC G++ P ++ Q E +K+L+ + + L +D ++ +S+K+ ++K
Sbjct: 177 GGATCDTAGIIQPAVQIVVAYQVTEALKILVEDFEALRETFLSFDIWNNQNMSIKVNKQK 236
Query: 362 KEDC 365
K+ C
Sbjct: 237 KDTC 240
>gnl|CDD|236320 PRK08644, PRK08644, thiamine biosynthesis protein ThiF;
Provisional.
Length = 212
Score = 119 bits (301), Expect = 4e-31
Identities = 54/132 (40%), Positives = 73/132 (55%), Gaps = 2/132 (1%)
Query: 147 QEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQP 206
EKL A V I G GG GS LA SGVG L L D+D VE SNL+RQ + IG P
Sbjct: 23 LEKLKKAKVGIAGAGGLGSNIAVALARSGVGNLKLVDFDVVEPSNLNRQQYFISQ-IGMP 81
Query: 207 KVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACL-R 265
KV + K + IN + A+ +D N ++ + D+VV+A DNA T+ +L + L
Sbjct: 82 KVEALKENLLEINPFVEIEAHNEKIDEDNIEELFKDCDIVVEAFDNAETKAMLVETVLEH 141
Query: 266 EGRPLVSASALG 277
G+ LV+AS +
Sbjct: 142 PGKKLVAASGMA 153
>gnl|CDD|238384 cd00755, YgdL_like, Family of activating enzymes (E1) of
ubiquitin-like proteins related to the E.coli
hypothetical protein ygdL. The common reaction mechanism
catalyzed by E1-like enzymes begins with a nucleophilic
attack of the C-terminal carboxylate of the
ubiquitin-like substrate, on the alpha-phosphate of an
ATP molecule bound at the active site of the activating
enzymes, leading to the formation of a high-energy
acyladenylate intermediate and subsequently to the
formation of a thiocarboxylate at the C termini of the
substrate. The exact function of this family is unknown.
Length = 231
Score = 109 bits (275), Expect = 2e-27
Identities = 53/132 (40%), Positives = 71/132 (53%), Gaps = 1/132 (0%)
Query: 143 GVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHT 202
G G EKL NA V +VG GG GS + LA SGVG L L D+D V +SNL+RQ+ T
Sbjct: 2 GEEGLEKLRNAHVAVVGLGGVGSWAAEALARSGVGKLTLIDFDVVCVSNLNRQIHALLST 61
Query: 203 IGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRR-YDVVVDACDNAPTRYLLND 261
+G+PKV I IN V A + L N+ D++ D VVDA D+ + L
Sbjct: 62 VGKPKVEVMAERIRDINPECEVDAVEEFLTPDNSEDLLGGDPDFVVDAIDSIRAKVALIA 121
Query: 262 ACLREGRPLVSA 273
C + P++S+
Sbjct: 122 YCRKRKIPVISS 133
>gnl|CDD|224100 COG1179, COG1179, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 1
[Coenzyme metabolism].
Length = 263
Score = 105 bits (264), Expect = 1e-25
Identities = 50/143 (34%), Positives = 72/143 (50%), Gaps = 3/143 (2%)
Query: 131 ERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELS 190
+R+ L G G EKL A V +VG GG GS ++ LA SG+G + L D D V ++
Sbjct: 11 QRFGGIARL--YGEDGLEKLKQAHVCVVGIGGVGSWAVEALARSGIGRITLIDMDDVCVT 68
Query: 191 NLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDII-RRYDVVVDA 249
N +RQ+ IG+PKV K I IN V A + N D++ + +D V+DA
Sbjct: 69 NTNRQIHALLGDIGKPKVEVMKERIKQINPECEVTAINDFITEENLEDLLSKGFDYVIDA 128
Query: 250 CDNAPTRYLLNDACLREGRPLVS 272
D+ + L C R P++S
Sbjct: 129 IDSVRAKVALIAYCRRNKIPVIS 151
>gnl|CDD|238764 cd01487, E1_ThiF_like, E1_ThiF_like. Member of superfamily of
activating enzymes (E1) of the ubiquitin-like proteins.
The common reaction mechanism catalyzed by E1-like
enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of the ubiquitin-like substrate,
on the alpha-phosphate of an ATP molecule bound at the
active site of the activating enzymes, leading to the
formation of a high-energy acyladenylate intermediate
and subsequently to the formation of a thiocarboxylate
at the C termini of the substrate. The exact function of
this family is unknown.
Length = 174
Score = 100 bits (252), Expect = 7e-25
Identities = 49/125 (39%), Positives = 69/125 (55%), Gaps = 2/125 (1%)
Query: 154 SVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAKR 213
V I G GG GS LA SGVG L L D+D VE SNL+RQ + IG+PKV + K
Sbjct: 1 KVGIAGAGGLGSNIAVLLARSGVGNLKLVDFDVVEPSNLNRQQYFLSQ-IGEPKVEALKE 59
Query: 214 FISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACLR-EGRPLVS 272
+ IN + A +D +N + D+VV+A DNA T+ +L ++ L + +P+V
Sbjct: 60 NLREINPFVKIEAINIKIDENNLEGLFGDCDIVVEAFDNAETKAMLAESLLGNKNKPVVC 119
Query: 273 ASALG 277
AS +
Sbjct: 120 ASGMA 124
>gnl|CDD|113988 pfam05237, MoeZ_MoeB, MoeZ/MoeB domain. This putative domain is
found in the MoeZ protein and the MoeB protein. The
domain has two CXXC motifs that are only partly
conserved.
Length = 77
Score = 83.8 bits (208), Expect = 6e-20
Identities = 39/79 (49%), Positives = 52/79 (65%), Gaps = 6/79 (7%)
Query: 292 CYRCIYPVPPPAETVGTCGDNGVLGPVPGVMGTLQAVETIKLL--IGLPVMDKLLVYDAE 349
CYRC++P PP + TC GVLGPV G +G+LQA+E IKLL IG P+ +LL++DA
Sbjct: 1 CYRCLFPEPPGSVP--TCATAGVLGPVVGTIGSLQALEAIKLLTGIGEPLSGRLLLFDAW 58
Query: 350 LSKFLSVKLRKKKEDC-VC 367
F ++LR + DC VC
Sbjct: 59 TMHFRKIRLR-RDPDCPVC 76
>gnl|CDD|162819 TIGR02354, thiF_fam2, thiamine biosynthesis protein ThiF, family 2.
Members of the HesA/MoeB/ThiF family of proteins
(pfam00899) include a number of members encoded in the
midst of thiamine biosynthetic operons. This mix of
known and putative ThiF proteins shows a deep split in
phylogenetic trees, with one the E. coli ThiF and the E.
coli MoeB proteins seemingly more closely related than
E. coli ThiF and Campylobacter (for example) ThiF. This
model represents the divergent clade of putative ThiF
proteins such found in Campylobacter [Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 200
Score = 86.5 bits (214), Expect = 2e-19
Identities = 50/131 (38%), Positives = 72/131 (54%), Gaps = 3/131 (2%)
Query: 148 EKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPK 207
+KL A+V I G GG GS LA +G+G L L D+D VE SNL+RQ + +G+PK
Sbjct: 17 QKLEQATVAICGLGGLGSNVAINLARAGIGKLILVDFDVVEPSNLNRQQYKASQ-VGEPK 75
Query: 208 VTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACLR-- 265
+ K IS IN T + AY + N + D+V +A DNA + +L +A L
Sbjct: 76 TEALKENISEINPYTEIEAYDEKITEENIDKFFKDADIVCEAFDNAEAKAMLVNAVLEKY 135
Query: 266 EGRPLVSASAL 276
+ + L++AS L
Sbjct: 136 KDKYLIAASGL 146
>gnl|CDD|238766 cd01489, Uba2_SUMO, Ubiquitin activating enzyme (E1) subunit UBA2.
UBA2 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. UBA2
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 312
Score = 83.2 bits (206), Expect = 1e-17
Identities = 49/150 (32%), Positives = 75/150 (50%), Gaps = 4/150 (2%)
Query: 155 VLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAKRF 214
VL+VG GG G ++ L +G G + + D D ++LSNL+RQ + +G+ K AK
Sbjct: 2 VLVVGAGGIGCELLKNLVLTGFGEIHIIDLDTIDLSNLNRQFLFRKKHVGKSKAQVAKEA 61
Query: 215 ISAINRNTIVHAYQ-TLLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACLREGRPLVSA 273
+ + N N + AY + D + +++D+V +A DN R +N CL PL+ +
Sbjct: 62 VLSFNPNVKIVAYHANIKDPDFNVEFFKQFDLVFNALDNLAARRHVNKMCLAADVPLIES 121
Query: 274 SALGLEGQLCVYNYKG-GPCYRCIYPVPPP 302
G GQ+ V KG CY C P P
Sbjct: 122 GTTGFLGQVQVI-KKGKTECYEC-QPKETP 149
>gnl|CDD|181302 PRK08223, PRK08223, hypothetical protein; Validated.
Length = 287
Score = 82.8 bits (205), Expect = 2e-17
Identities = 50/164 (30%), Positives = 76/164 (46%), Gaps = 4/164 (2%)
Query: 128 DITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRV 187
D E + R + + Q++L N+ V I G GG G + LA G+G +AD+D
Sbjct: 5 DYDEAFCRNLGW--ITPTEQQRLRNSRVAIAGLGGVGGIHLLTLARLGIGKFTIADFDVF 62
Query: 188 ELSNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVV 247
EL N +RQ T+G+PK + IN + A+ + NA + DV V
Sbjct: 63 ELRNFNRQAGAMMSTLGRPKAEVLAEMVRDINPELEIRAFPEGIGKENADAFLDGVDVYV 122
Query: 248 DACD--NAPTRYLLNDACLREGRPLVSASALGLEGQLCVYNYKG 289
D D R L+ AC + G P ++A+ LG+ L V++ G
Sbjct: 123 DGLDFFEFDARRLVFAACQQRGIPALTAAPLGMGTALLVFDPGG 166
>gnl|CDD|238761 cd01484, E1-2_like, Ubiquitin activating enzyme (E1), repeat
2-like. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets them
for degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. A set of novel molecules
with a structural similarity to Ub, called Ub-like
proteins (Ubls), have similar conjugation cascades. In
contrast to ubiquitin-E1, which is a single-chain
protein with a weakly conserved two-fold repeat, many of
the Ubls-E1are a heterodimer where each subunit
corresponds to one half of a single-chain E1. This CD
represents the family homologous to the second repeat of
Ub-E1.
Length = 234
Score = 79.2 bits (195), Expect = 9e-17
Identities = 43/150 (28%), Positives = 68/150 (45%), Gaps = 2/150 (1%)
Query: 154 SVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAKR 213
VL+VG GG G ++ LA G G + + D D +++SNL+RQ + IG+PK A
Sbjct: 1 KVLLVGAGGIGCELLKNLALMGFGQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKSEVAAE 60
Query: 214 FISAINRNTIVHAYQ-TLLDTSNACD-IIRRYDVVVDACDNAPTRYLLNDACLREGRPLV 271
++ N N V YQ + + D ++ ++V+A DN R +N + PL+
Sbjct: 61 AVNDRNPNCKVVPYQNKVGPEQDFNDTFFEQFHIIVNALDNIIARRYVNGMLIFLIVPLI 120
Query: 272 SASALGLEGQLCVYNYKGGPCYRCIYPVPP 301
+ G +G V C C P
Sbjct: 121 ESGTEGFKGNAQVILPGMTECIECTLYPPQ 150
>gnl|CDD|238784 cd01526, RHOD_ThiF, Member of the Rhodanese Homology Domain
superfamily. This CD includes several putative
molybdopterin synthase sulfurylases including the
molybdenum cofactor biosynthetic protein (CnxF) of
Aspergillus nidulans and the molybdenum cofactor
synthesis protein 3 (MOCS3) of Homo sapiens. These
rhodanese-like domains are found C-terminal of the ThiF
and MoeZ_MoeB domains.
Length = 122
Score = 75.4 bits (186), Expect = 2e-16
Identities = 42/131 (32%), Positives = 60/131 (45%), Gaps = 11/131 (8%)
Query: 395 ILDPTEHLTALDYRDEFLARRVAHTLLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGE 454
+L P E ++ DY+ L H LLDVR F + L A + ++++ AE
Sbjct: 3 LLSPEERVSVKDYK-NILQAGKKHVLLDVRPKVHFEICRLPEAINIPLSELLSKAAELKS 61
Query: 455 CPAFLESLREDILAHRHVFVICRRGNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGW 514
L+ L D ++V+CRRGNDSQ V+ LK G+ +R+I G K W
Sbjct: 62 ----LQELPLDNDKDSPIYVVCRRGNDSQTAVRKLKEL------GLERFVRDIIGGLKAW 111
Query: 515 QKYVDNRIPTY 525
VD P Y
Sbjct: 112 ADKVDPTFPLY 122
>gnl|CDD|130475 TIGR01408, Ube1, ubiquitin-activating enzyme E1. This model
represents the full length, over a thousand amino acids,
of a multicopy family of eukaryotic proteins, many of
which are designated ubiquitin-activating enzyme E1.
Members have two copies of the ThiF family domain
(pfam00899), a repeat found in ubiquitin-activating
proteins (pfam02134), and other regions.
Length = 1008
Score = 80.3 bits (198), Expect = 8e-16
Identities = 52/158 (32%), Positives = 80/158 (50%), Gaps = 11/158 (6%)
Query: 132 RYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGT-----LGLADYDR 186
RY QI + G Q+KL N ++ +VGCG G ++ A GVGT + + D D
Sbjct: 401 RYDAQIAV--FGDTFQQKLQNLNIFLVGCGAIGCEMLKNFALMGVGTGKKGMITVTDPDL 458
Query: 187 VELSNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLL--DTSNACD--IIRR 242
+E SNL+RQ + H IG+PK +A IN + A+Q + +T + +
Sbjct: 459 IEKSNLNRQFLFRPHHIGKPKSYTAADATLKINPQIKIDAHQNRVGPETETIFNDEFYEK 518
Query: 243 YDVVVDACDNAPTRYLLNDACLREGRPLVSASALGLEG 280
DVV++A DN R ++ CL +PL+ + LG +G
Sbjct: 519 LDVVINALDNVEARRYVDSRCLAFLKPLLESGTLGTKG 556
Score = 46.4 bits (110), Expect = 3e-05
Identities = 37/155 (23%), Positives = 70/155 (45%), Gaps = 14/155 (9%)
Query: 133 YSRQILLDQVGVMGQE---KLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVEL 189
YSRQ+ V+G E K+ ++VLI G GG G + L +GV ++ L D ++ +
Sbjct: 7 YSRQLY-----VLGDEAMQKMAKSNVLISGMGGLGLEIAKNLVLAGVKSVTLHDTEKCQA 61
Query: 190 SNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDA 249
+L + +G+ + + + ++ +N V + + + ++ VV
Sbjct: 62 WDLSSNFFLSEDDVGRNRAEAVVKKLAELNPYVHV----SSSSVPFNEEFLDKFQCVVLT 117
Query: 250 CDNAPTRYLLNDACLREGRPL--VSASALGLEGQL 282
+ P + +ND C + P+ +SA GL G L
Sbjct: 118 EMSLPLQKEINDFCHSQCPPIAFISADVRGLFGSL 152
>gnl|CDD|238767 cd01490, Ube1_repeat2, Ubiquitin activating enzyme (E1), repeat 2.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the second repeat of Ub-E1.
Length = 435
Score = 69.6 bits (171), Expect = 9e-13
Identities = 39/136 (28%), Positives = 64/136 (47%), Gaps = 9/136 (6%)
Query: 154 SVLIVGCGGTGSPCIQYLAASGVGT-----LGLADYDRVELSNLHRQVIHTTHTIGQPKV 208
V +VG G G ++ A GVGT + + D D +E SNL+RQ + H +G+PK
Sbjct: 1 KVFLVGAGAIGCELLKNFALMGVGTGESGEITVTDMDNIEKSNLNRQFLFRPHDVGKPKS 60
Query: 209 TSAKRFISAINRNTIVHAYQTLLDTSNAC----DIIRRYDVVVDACDNAPTRYLLNDACL 264
A + A+N + + A Q + + + D V +A DN R ++ C+
Sbjct: 61 EVAAAAVKAMNPDLKITALQNRVGPETEHIFNDEFWEKLDGVANALDNVDARMYVDRRCV 120
Query: 265 REGRPLVSASALGLEG 280
+PL+ + LG +G
Sbjct: 121 YYRKPLLESGTLGTKG 136
>gnl|CDD|238762 cd01485, E1-1_like, Ubiquitin activating enzyme (E1), repeat
1-like. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets them
for degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. The E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. A set of novel molecules
with a structural similarity to Ub, called Ub-like
proteins (Ubls), have similar conjugation cascades. In
contrast to ubiquitin-E1, which is a single-chain
protein with a weakly conserved two-fold repeat, many of
the Ubls-E1are a heterodimer where each subunit
corresponds to one half of a single-chain E1. This CD
represents the family homologous to the first repeat of
Ub-E1.
Length = 198
Score = 62.4 bits (152), Expect = 3e-11
Identities = 38/154 (24%), Positives = 72/154 (46%), Gaps = 6/154 (3%)
Query: 133 YSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNL 192
Y RQI L G Q KL +A VLI+G G G+ + L +G+ ++ + D+ V +L
Sbjct: 2 YDRQIRL--WGDEAQNKLRSAKVLIIGAGALGAEIAKNLVLAGIDSITIVDHRLVSTEDL 59
Query: 193 HRQ-VIHTTHT-IGQPKVTSAKRFISAINRNTIVHAYQ--TLLDTSNACDIIRRYDVVVD 248
+ + G + ++ F+ +N N + + +L + SN + ++++ +V+
Sbjct: 60 GSNFFLDAEVSNSGMNRAAASYEFLQELNPNVKLSIVEEDSLSNDSNIEEYLQKFTLVIA 119
Query: 249 ACDNAPTRYLLNDACLREGRPLVSASALGLEGQL 282
+N +ND C + P +S + GL G
Sbjct: 120 TEENYERTAKVNDVCRKHHIPFISCATYGLIGYA 153
>gnl|CDD|185071 PRK15116, PRK15116, sulfur acceptor protein CsdL; Provisional.
Length = 268
Score = 63.3 bits (154), Expect = 4e-11
Identities = 38/131 (29%), Positives = 58/131 (44%), Gaps = 3/131 (2%)
Query: 153 ASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAK 212
A + +VG GG GS + LA +G+G + L D D V ++N +RQ+ +G K
Sbjct: 31 AHICVVGIGGVGSWAAEALARTGIGAITLIDMDDVCVTNTNRQIHALRDNVGLAKAEVMA 90
Query: 213 RFISAINRNTIVHAYQTLLDTSNACDII-RRYDVVVDACDNAPTRYLLNDACLREGRPLV 271
I IN V + N + + + V+DA D+ + L C R PLV
Sbjct: 91 ERIRQINPECRVTVVDDFITPDNVAEYMSAGFSYVIDAIDSVRPKAALIAYCRRNKIPLV 150
Query: 272 SASALGLEGQL 282
+ G GQ+
Sbjct: 151 TTGGAG--GQI 159
>gnl|CDD|238768 cd01491, Ube1_repeat1, Ubiquitin activating enzyme (E1), repeat 1.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the first repeat of Ub-E1.
Length = 286
Score = 62.3 bits (152), Expect = 9e-11
Identities = 42/153 (27%), Positives = 68/153 (44%), Gaps = 12/153 (7%)
Query: 133 YSRQILLDQVGVMGQE---KLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVEL 189
YSRQ+ V+G E KL ++VLI G GG G + L +GV ++ L D
Sbjct: 2 YSRQL-----YVLGHEAMKKLQKSNVLISGLGGLGVEIAKNLILAGVKSVTLHDTKPCSW 56
Query: 190 SNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDA 249
S+L Q IG+ + +++ ++ +N V L T D + ++ VVV
Sbjct: 57 SDLSSQFYLREEDIGKNRAEASQARLAELNPYVPVTVSTGPLTT----DELLKFQVVVLT 112
Query: 250 CDNAPTRYLLNDACLREGRPLVSASALGLEGQL 282
+ + +N+ C G +SA GL G +
Sbjct: 113 DASLEDQLKINEFCHSPGIKFISADTRGLFGSI 145
>gnl|CDD|238765 cd01488, Uba3_RUB, Ubiquitin activating enzyme (E1) subunit UBA3.
UBA3 is part of the heterodimeric activating enzyme
(E1), specific for the Rub family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins. consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin(-like) by C-terminal adenylation, and
subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis. UBA3
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 291
Score = 57.0 bits (138), Expect = 6e-09
Identities = 38/164 (23%), Positives = 70/164 (42%), Gaps = 9/164 (5%)
Query: 154 SVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAKR 213
+L++G GG G ++ LA SG + + D D +++SNL+RQ + IG+PK A +
Sbjct: 1 KILVIGAGGLGCELLKNLALSGFRNIHVIDMDTIDVSNLNRQFLFREKDIGKPKAEVAAK 60
Query: 214 FISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACLREGR----- 268
F++ V + + + + R++++++ D+ R +N +
Sbjct: 61 FVNDRVPGVNVTPHFGKIQDKDE-EFYRQFNIIICGLDSIEARRWINGTLVSLLLYEDPE 119
Query: 269 ---PLVSASALGLEGQLCVYNYKGGPCYRCIYPVPPPAETVGTC 309
PL+ G +G V C C + PP T C
Sbjct: 120 SIIPLIDGGTEGFKGHARVILPGITACIECSLDLFPPQVTFPLC 163
>gnl|CDD|184854 PRK14852, PRK14852, hypothetical protein; Provisional.
Length = 989
Score = 56.6 bits (136), Expect = 2e-08
Identities = 55/199 (27%), Positives = 87/199 (43%), Gaps = 12/199 (6%)
Query: 133 YSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNL 192
+SR + L V GQ +LL + V I G GG G + LA +G+G LAD+D NL
Sbjct: 315 FSRNLGL--VDYAGQRRLLRSRVAIAGLGGVGGIHLMTLARTGIGNFNLADFDAYSPVNL 372
Query: 193 HRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDN 252
+RQ + + G+ K+ ++N + ++ + ++ D++VD D
Sbjct: 373 NRQYGASIASFGRGKLDVMTERALSVNPFLDIRSFPEGVAAETIDAFLKDVDLLVDGIDF 432
Query: 253 AP---TRYLLNDACLREGRPLVSASALGLEGQLCVYNYKGGPCYRCIYPV---PPPAETV 306
R L N A L G P+++A LG L V+ GG + + + PP E
Sbjct: 433 FALDIRRRLFNRA-LELGIPVITAGPLGYSCALLVF-MPGGMNFDSYFGIDDDTPPMEGY 490
Query: 307 GTCGDNGVLGPVPGVMGTL 325
G L P P +G +
Sbjct: 491 LRFGMG--LAPRPAHLGYM 507
>gnl|CDD|184853 PRK14851, PRK14851, hypothetical protein; Provisional.
Length = 679
Score = 56.4 bits (136), Expect = 3e-08
Identities = 49/163 (30%), Positives = 76/163 (46%), Gaps = 8/163 (4%)
Query: 131 ERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELS 190
+SR I L G QE+L A V I G GG G + + +G+G +AD+D+ E
Sbjct: 24 AAFSRNIGLFTPG--EQERLAEAKVAIPGMGGVGGVHLITMVRTGIGRFHIADFDQFEPV 81
Query: 191 NLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDAC 250
N++RQ + G+PK+ K +IN + + ++ N + DVV+D
Sbjct: 82 NVNRQFGARVPSFGRPKLAVMKEQALSINPFLEITPFPAGINADNMDAFLDGVDVVLDGL 141
Query: 251 DNAP---TRYLLNDACLRE-GRPLVSASALGLEGQLCVYNYKG 289
D R L N A RE G P+++A LG + V+ +G
Sbjct: 142 DFFQFEIRRTLFNMA--REKGIPVITAGPLGYSSAMLVFTPQG 182
>gnl|CDD|238769 cd01492, Aos1_SUMO, Ubiquitin activating enzyme (E1) subunit Aos1.
Aos1 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. Aos1
contains part of the adenylation domain.
Length = 197
Score = 50.4 bits (121), Expect = 3e-07
Identities = 37/148 (25%), Positives = 66/148 (44%), Gaps = 3/148 (2%)
Query: 133 YSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNL 192
Y RQI L G+ Q++L +A +L++G G G+ + L SG+G+L + D V +L
Sbjct: 4 YDRQIRL--WGLEAQKRLRSARILLIGLKGLGAEIAKNLVLSGIGSLTILDDRTVTEEDL 61
Query: 193 HRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQTLLDTSNACDIIRRYDVVVDACDN 252
Q + +GQ + ++ + A+N V + + ++DVVV +
Sbjct: 62 GAQFLIPAEDLGQNRAEASLERLRALNPRVKVSVDTDDISEKPE-EFFSQFDVVVATELS 120
Query: 253 APTRYLLNDACLREGRPLVSASALGLEG 280
+N+ C + G + GL G
Sbjct: 121 RAELVKINELCRKLGVKFYATGVHGLFG 148
>gnl|CDD|197731 smart00450, RHOD, Rhodanese Homology Domain. An alpha beta fold
found duplicated in the Rhodanese protein. The the
Cysteine containing enzymatically active version of the
domain is also found in the CDC25 class of protein
phosphatases and a variety of proteins such as sulfide
dehydrogenases and stress proteins such as Senesence
specific protein 1 in plants, PspE and GlpE in bacteria
and cyanide and arsenate resistance proteins. Inactive
versions with a loss of the cysteine are also seen in
Dual specificity phosphatases, ubiquitin hydrolases from
yeast and in sulfuryltransferases. These are likely to
play a role in protein interactions.
Length = 100
Score = 46.7 bits (111), Expect = 1e-06
Identities = 24/102 (23%), Positives = 38/102 (37%), Gaps = 7/102 (6%)
Query: 418 HTLLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVICR 477
LLDVRS +E+ + A + ++++ E R + + V V CR
Sbjct: 5 VVLLDVRSPEEYEGGHIPGAVNIPLSELLDRRGELDILEFEELLKRLGLDKDKPVVVYCR 64
Query: 478 RGNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQKYVD 519
GN S K LL+ ++ + GYK W
Sbjct: 65 SGNRSAKAAWLLREL-GFK------NVYLLDGGYKEWSAAGP 99
>gnl|CDD|236122 PRK07877, PRK07877, hypothetical protein; Provisional.
Length = 722
Score = 51.1 bits (123), Expect = 1e-06
Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 2/105 (1%)
Query: 171 LAASGV-GTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAYQT 229
LAA G+ G L LAD+D +ELSNL+R V +G K A R I+ ++ V +
Sbjct: 125 LAAEGLCGELRLADFDTLELSNLNR-VPAGVFDLGVNKAVVAARRIAELDPYLPVEVFTD 183
Query: 230 LLDTSNACDIIRRYDVVVDACDNAPTRYLLNDACLREGRPLVSAS 274
L N + DVVV+ CD+ + LL +A P++ A+
Sbjct: 184 GLTEDNVDAFLDGLDVVVEECDSLDVKVLLREAARARRIPVLMAT 228
>gnl|CDD|238089 cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold
domain found duplicated in the rhodanese protein. The
cysteine containing enzymatically active version of the
domain is also found in the Cdc25 class of protein
phosphatases and a variety of proteins such as sulfide
dehydrogenases and certain stress proteins such as
senesence specific protein 1 in plants, PspE and GlpE in
bacteria and cyanide and arsenate resistance proteins.
Inactive versions (no active site cysteine) are also
seen in dual specificity phosphatases, ubiquitin
hydrolases from yeast and in sulfuryltransferases, where
they are believed to play a regulatory role in
multidomain proteins.
Length = 89
Score = 45.0 bits (107), Expect = 3e-06
Identities = 19/97 (19%), Positives = 41/97 (42%), Gaps = 19/97 (19%)
Query: 419 TLLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVICRR 478
LLDVR +E+A + A + ++++ + ++ + + V CR
Sbjct: 12 VLLDVREPEEYAAGHIPGAINIPLSEL------------EERAALLELDKDKPIVVYCRS 59
Query: 479 GNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQ 515
GN S + +LL++ ++ N++ G W+
Sbjct: 60 GNRSARAAKLLRKA-------GGTNVYNLEGGMLAWK 89
>gnl|CDD|238770 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit
APPBP1. APPBP1 is part of the heterodimeric activating
enzyme (E1), specific for the Rub family of
ubiquitin-like proteins (Ubls). E1 enzymes are part of a
conjugation cascade to attach Ub or Ubls, covalently to
substrate proteins consisting of activating (E1),
conjugating (E2), and/or ligating (E3) enzymes. E1
activates ubiquitin(-like) by C-terminal adenylation,
and subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis.
ABPP1 contains part of the adenylation domain.
Length = 425
Score = 46.9 bits (112), Expect = 2e-05
Identities = 33/160 (20%), Positives = 67/160 (41%), Gaps = 10/160 (6%)
Query: 131 ERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELS 190
++Y RQ+ L G GQ L +A V ++ TG+ ++ L G+G+ + D +V+
Sbjct: 1 QKYDRQLRL--WGEHGQAALESAHVCLLNATATGTEILKNLVLPGIGSFTIVDGSKVDEE 58
Query: 191 NLHRQVIHTTHTIGQPKVTSAKRFI----SAINRNTIVHAYQTLLDTSNACDIIRRYDVV 246
+L ++G+ + + + +N + + + + LLD ++ VV
Sbjct: 59 DLGNNFFLDASSLGKSRAEATCELLQELNPDVNGSAVEESPEALLDND--PSFFSQFTVV 116
Query: 247 VDACDNAPTRYLLNDACLREGRPLVSASALGLEG--QLCV 284
+ T L D PL+ + GL G ++ +
Sbjct: 117 IATNLPESTLLRLADVLWSANIPLLYVRSYGLYGYIRIQL 156
>gnl|CDD|216005 pfam00581, Rhodanese, Rhodanese-like domain. Rhodanese has an
internal duplication. This Pfam represents a single copy
of this duplicated domain. The domain is found as a
single copy in other proteins, including phosphatases
and ubiquitin C-terminal hydrolases.
Length = 106
Score = 42.1 bits (99), Expect = 5e-05
Identities = 23/101 (22%), Positives = 42/101 (41%), Gaps = 15/101 (14%)
Query: 420 LLDVRSVDEFAMM----SLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVI 475
L+DVRS +E+A ++NI D + + LE L + + + + V
Sbjct: 16 LIDVRSPEEYAKGHIPGAVNIPLSLPSLD---------KLESELEELGKKLDKDKTIVVY 66
Query: 476 CRRGNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQK 516
C GN S + LL + G ++ + G++ W+
Sbjct: 67 CASGNRSGQAAALL-LALILKALGYK-NVYVLDGGFEAWKA 105
>gnl|CDD|223680 COG0607, PspE, Rhodanese-related sulfurtransferase [Inorganic ion
transport and metabolism].
Length = 110
Score = 40.7 bits (95), Expect = 2e-04
Identities = 19/117 (16%), Positives = 35/117 (29%), Gaps = 20/117 (17%)
Query: 410 EFLARRVAHTLLDVRSVDEFAMMS-LNIASHATMADVQLMFAEAGECPAFLESLREDILA 468
L LLDVR +E+ A + +++++ ++
Sbjct: 13 ALLLAGEDAVLLDVREPEEYERGHIPGAAINIPLSELKAAENLL------------ELPD 60
Query: 469 HRHVFVICRRGNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQKYVDNRIPTY 525
+ V C G S LK G ++ N+ G W+ + Y
Sbjct: 61 DDPIVVYCASGVRSAAAAAALKLA------GFT-NVYNLDGGIDAWKGAGLPLVRGY 110
>gnl|CDD|163448 TIGR03736, PRTRC_ThiF, PRTRC system ThiF family protein. A novel
genetic system characterized by six major proteins,
included a ParB homolog and a ThiF homolog, is
designated PRTRC, or ParB-Related,ThiF-Related Cassette.
This family is the PRTRC system ThiF family protein.
Length = 244
Score = 39.3 bits (92), Expect = 0.003
Identities = 38/119 (31%), Positives = 52/119 (43%), Gaps = 27/119 (22%)
Query: 154 SVLIVGCGGTGSPCIQYLA-------ASGVGTLGLA----DYDRVELSNLHRQVIHTTHT 202
SV++VG GGTGS I LA A G GLA D D V +N+ RQ +
Sbjct: 13 SVVLVGAGGTGSQVIAGLARLHHALKALG-HPGGLAVTVYDDDTVSEANVGRQAFY-PAD 70
Query: 203 IGQPKVTSAKRFISAINR-----NTIVHAYQTLLDTSNACDIIRRYDVVVDACDNAPTR 256
+GQ K I +NR T A+ ++ S+ + R D+V+ DN R
Sbjct: 71 VGQNKA------IVLVNRLNQAMGTDWTAHPERVERSST---LHRPDIVIGCVDNRAAR 120
>gnl|CDD|238786 cd01528, RHOD_2, Member of the Rhodanese Homology Domain
superfamily, subgroup 2. Subgroup 2 includes
uncharacterized putative rhodanese-related domains.
Length = 101
Score = 35.8 bits (83), Expect = 0.008
Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 22/102 (21%)
Query: 420 LLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVICRRG 479
L+DVR +E + L H M+++ + + V+C G
Sbjct: 20 LIDVREPEELEIAFLPGFLHLPMSEIPE------RSKELDSDNPDK-----DIVVLCHHG 68
Query: 480 NDSQKVVQLLKR--YVERHRPGVVYDIRNIKEGYKGWQKYVD 519
S +V Q L R + + N++ G W VD
Sbjct: 69 GRSMQVAQWLLRQGFEN---------VYNLQGGIDAWSLEVD 101
>gnl|CDD|217020 pfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain.
This domain is found associated with the Pfam tRNA
synthetase class II domain (pfam00587) and represents
the N-terminal domain of seryl-tRNA synthetase.
Length = 108
Score = 34.1 bits (79), Expect = 0.038
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 2 DTEEAVRKVAQLKEKIRQLKEDLTNAETELETIL 35
D E + +V +LK++++ L+ +L E EL+ +L
Sbjct: 68 DAEALIAEVKELKDELKALEAELRELEAELDKLL 101
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 35.0 bits (82), Expect = 0.091
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 2 DTEEAVRKVAQLKEKIRQLKEDLTNAETELETIL 35
D E + +V +LKE+I+ L+ +L E ELE +L
Sbjct: 67 DAEALIAEVKELKEEIKALEAELDELEAELEELL 100
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.
This model family represents the major capsid protein
component of the heads (capsids) of bacteriophage HK97,
phi-105, P27, and related phage. This model represents
one of several analogous families lacking detectable
sequence similarity. The gene encoding this component is
typically located in an operon encoding the small and
large terminase subunits, the portal protein and the
prohead or maturation protease [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 384
Score = 33.5 bits (77), Expect = 0.23
Identities = 18/100 (18%), Positives = 31/100 (31%), Gaps = 10/100 (10%)
Query: 1 MDTEEAVRKVAQLKEKIRQLKEDLTNAETELETILEDRAFKSRPTDGASVRDDTIRRDVS 60
+ EE + LKE+I +L ++ E L+ + A G ++ + +
Sbjct: 25 AEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAAS--GEGGGGEEEEEEAKAEA 82
Query: 61 NERDT---NGAGQRGAHSTDSQVGDPAS-----PEEIHRE 92
E G G + PEE E
Sbjct: 83 AEFRAYLRGGDDALAEERKALSTGTDSDGGYLVPEEFSTE 122
>gnl|CDD|205039 pfam12718, Tropomyosin_1, Tropomyosin like. This family is a set
of eukaryotic tropomyosins. Within the yeast Tmp1 and
Tmp2, biochemical and sequence analyses indicate that
Tpm2p spans four actin monomers along a filament,
whereas Tpmlp spans five. Despite its shorter length,
Tpm2p can compete with Tpm1p for binding to F-actin.
Over-expression of Tpm2p in vivo alters the axial
budding of haploids to a bipolar pattern, and this can
be partially suppressed by co-over-expression of Tpm1p.
This suggests distinct functions for the two
tropomyosins, and indicates that the ratio between them
is important for correct morphogenesis. The family also
contains higher eukaryote Tmp3 members.
Length = 143
Score = 32.2 bits (74), Expect = 0.23
Identities = 8/31 (25%), Positives = 20/31 (64%)
Query: 1 MDTEEAVRKVAQLKEKIRQLKEDLTNAETEL 31
++ E A + +L+EK+++L+++ E E+
Sbjct: 7 LEAENAQERAEELEEKLKELEQENLEKEQEI 37
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 33.5 bits (77), Expect = 0.28
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 154 SVLIVGCGGTGSPCIQYLAASGVGTLGLAD 183
+L++G GG GS LA +G G + +AD
Sbjct: 3 KILVIGAGGVGSVVAHKLAQNGDGEVTIAD 32
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 33.4 bits (77), Expect = 0.29
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 155 VLIVGCGGTGSPCIQYLAASGVGTLGLADYDR 186
VLI+G GG G LA G + +AD
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRSL 32
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 32.9 bits (76), Expect = 0.36
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 155 VLIVGCGGTGSPCIQYLAASG 175
V +VG GG G +QY A G
Sbjct: 170 VAVVGAGGLGHMAVQYAKAMG 190
>gnl|CDD|238780 cd01522, RHOD_1, Member of the Rhodanese Homology Domain
superfamily, subgroup 1. This CD includes the putative
rhodanese-related sulfurtransferases of several
uncharacterized proteins.
Length = 117
Score = 31.1 bits (71), Expect = 0.38
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 456 PAFLESLREDILAHRHVFVICRRGNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKG 513
P FL L E + R V ++CR GN S + + VY N+ EG++G
Sbjct: 51 PNFLAELEEKVGKDRPVLLLCRSGNRSIAAAEAA----AQAGFTNVY---NVLEGFEG 101
>gnl|CDD|238781 cd01523, RHOD_Lact_B, Member of the Rhodanese Homology Domain
superfamily. This CD includes predicted proteins with
rhodanese-like domains found N-terminal of the
metallo-beta-lactamase domain.
Length = 100
Score = 30.9 bits (70), Expect = 0.41
Identities = 23/96 (23%), Positives = 37/96 (38%), Gaps = 14/96 (14%)
Query: 419 TLLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGECPAFLESLREDILAHRHVFVICRR 478
+LDVR+ ++ + + T E E + + + + V VIC +
Sbjct: 17 FILDVRNESDYERWKI-DGENNTPYFDPYFDFLEIE-----EDILDQLPDDQEVTVICAK 70
Query: 479 GNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGW 514
SQ V +LL ER YD+ + G K W
Sbjct: 71 EGSSQFVAELLA---ERG-----YDVDYLAGGMKAW 98
>gnl|CDD|233388 TIGR01381, E1_like_apg7, E1-like protein-activating enzyme
Gsa7p/Apg7p. This model represents a family of
eukaryotic proteins found in animals, plants, and
yeasts, including Apg7p (YHR171W) from Saccharomyces
cerevisiae and GSA7 from Pichia pastoris. Members are
about 650 to 700 residues in length and include a
central domain of about 150 residues shared with the
ThiF/MoeB/HesA family of proteins. A low level of
similarity to ubiquitin-activating enzyme E1 is
described in a paper on peroxisome autophagy mediated by
GSA7, and is the basis of the name ubiquitin activating
enzyme E1-like protein. Members of the family appear to
be involved in protein lipidation events analogous to
ubiquitination and required for membrane fusion events
during autophagy.
Length = 664
Score = 32.6 bits (74), Expect = 0.62
Identities = 36/152 (23%), Positives = 56/152 (36%), Gaps = 21/152 (13%)
Query: 148 EKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTI---G 204
E+ VL++G G G + L GV + D +V SN RQ + G
Sbjct: 334 ERYSQLKVLLLGAGTLGCNVARCLIGWGVRHITFVDNGKVSYSNPVRQSLSNFEDCLLGG 393
Query: 205 QPKVTSA----KRFISAINRNTIVHAY-------------QTLLDTSNACDIIRRYDVVV 247
+ K +A KR +I + D + +I+ +DVV
Sbjct: 394 RGKAETAQKALKRIFPSIQATGHRLTVPMPGHPIDEKDVPELEKDIARLEQLIKDHDVVF 453
Query: 248 DACDNAPTRYLLNDACLREGRPLVSASALGLE 279
D+ R+L C R + +SA ALG +
Sbjct: 454 LLLDSREARWLPTVLCSRHKKIAISA-ALGFD 484
>gnl|CDD|219737 pfam08172, CASP_C, CASP C terminal. This domain is the
C-terminal region of the CASP family of proteins. It is
a Golgi membrane protein which is thought to have a
role in vesicle transport.
Length = 245
Score = 31.6 bits (72), Expect = 0.74
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 9/81 (11%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAETELETILEDRAFKSRPTDGASVRDDTIRRDVSNER 63
EE ++++ L K+ + +E E +L T+ +D R D AS+ R
Sbjct: 2 EELQKELSSLNAKLEEQQELNAKLENDLATV-QDEISNRRFNDNASMIS-------GGTR 53
Query: 64 DTNGAGQRGAHS-TDSQVGDP 83
G G S T S +G P
Sbjct: 54 RIPNRGGSGKLSPTSSIIGGP 74
>gnl|CDD|235717 PRK06153, PRK06153, hypothetical protein; Provisional.
Length = 393
Score = 31.9 bits (73), Expect = 0.75
Identities = 16/47 (34%), Positives = 22/47 (46%)
Query: 148 EKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHR 194
KL + I+G GGTGS + +A + V + L D D N R
Sbjct: 172 AKLEGQRIAIIGLGGTGSYILDLVAKTPVREIHLFDGDDFLQHNAFR 218
>gnl|CDD|238721 cd01444, GlpE_ST, GlpE sulfurtransferase (ST) and homologs are
members of the Rhodanese Homology Domain superfamily.
Unlike other rhodanese sulfurtransferases, GlpE is a
single domain protein but indications are that it
functions as a dimer. The active site contains a
catalytically active cysteine.
Length = 96
Score = 29.9 bits (68), Expect = 0.76
Identities = 30/110 (27%), Positives = 44/110 (40%), Gaps = 23/110 (20%)
Query: 409 DEFLARRVAHTLLDVRSVDEFAMMSLNI--ASHATMADVQLMFAEAGECPAFLESLREDI 466
E LA A LLDVR +A + +I A H + +L L D
Sbjct: 8 AELLAAGEAPVLLDVRDPASYAALPDHIPGAIHLDEDSL----------DDWLGDLDRD- 56
Query: 467 LAHRHVFVICRRGNDSQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQK 516
R V V C GN S ++ Q L E D+R++ G++ W++
Sbjct: 57 ---RPVVVYCYHGNSSAQLAQAL---REAGFT----DVRSLAGGFEAWRR 96
>gnl|CDD|234703 PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
Length = 278
Score = 31.7 bits (73), Expect = 0.84
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 152 NASVLIVGCGGTGSPCIQYLAASGVGTL 179
+LI+G GG I L GV +
Sbjct: 123 GKRILILGAGGAARAVILPLLDLGVAEI 150
>gnl|CDD|232908 TIGR00292, TIGR00292, thiazole biosynthesis enzyme. This enzyme is
involved in the biosynthesis of the thiamine precursor
thiazole, and is repressed by thiamine. This family
includes c-thi1, a Citrus gene induced during natural
and ethylene induced fruit maturation and is highly
homologous to plant and yeast thi genes involved in
thiamine biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Thiamine].
Length = 254
Score = 31.7 bits (72), Expect = 0.85
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 10/57 (17%)
Query: 123 SKFSKDITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTL 179
SK S+ I ERY +L + V+IVG G +G YLA +G+
Sbjct: 2 SKISRAIVERYFEDLL----------DYAESDVIIVGAGPSGLTAAYYLAKNGLKVC 48
>gnl|CDD|238763 cd01486, Apg7, Apg7 is an E1-like protein, that activates two
different ubiquitin-like proteins, Apg12 and Apg8, and
assigns them to specific E2 enzymes, Apg10 and Apg3,
respectively. This leads to the covalent conjugation of
Apg8 with phosphatidylethanolamine, an important step in
autophagy. Autophagy is a dynamic membrane phenomenon
for bulk protein degradation in the lysosome/vacuole.
Length = 307
Score = 31.6 bits (72), Expect = 0.91
Identities = 36/143 (25%), Positives = 59/143 (41%), Gaps = 20/143 (13%)
Query: 154 SVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTI--GQPKVTSA 211
L++G G G + L GV + D +V SN RQ + T G+PK +A
Sbjct: 1 KCLLLGAGTLGCNVARNLLGWGVRHITFVDSGKVSYSNPVRQSLFTFEDCKGGKPKAEAA 60
Query: 212 ----KRFISAINRNTIV-------H------AYQTLLDTSNACDIIRRYDVVVDACDNAP 254
K +I+ IV H TL D ++I+ +DV+ D+
Sbjct: 61 AERLKEIFPSIDATGIVLSIPMPGHPISESEVPSTLKDVKRLEELIKDHDVIFLLTDSRE 120
Query: 255 TRYLLNDACLREGRPLVSASALG 277
+R+L + + +++A ALG
Sbjct: 121 SRWLPTLLSAAKNKLVINA-ALG 142
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 31.4 bits (72), Expect = 1.0
Identities = 24/126 (19%), Positives = 49/126 (38%), Gaps = 29/126 (23%)
Query: 418 HTLLDVRSVDEFAM----MSLNIA--SHATMADVQLMFAE--------------AGECPA 457
L+DVRS EFA ++N+ + A+V ++ + + A
Sbjct: 3 DPLIDVRSPAEFAEGHLPGAINLPLLNDEERAEVGTLYKQVGPFAAIKLGLALVSPNLAA 62
Query: 458 FLESLREDILAHRHVFVICRRGND-SQKVVQLLKRYVERHRPGVVYDIRNIKEGYKGWQK 516
+E R + C RG S + LL + + + ++ GYK +++
Sbjct: 63 HVEQWRAFADGPPQPLLYCWRGGMRSGSLAWLLA--------QIGFRVPRLEGGYKAYRR 114
Query: 517 YVDNRI 522
+V +++
Sbjct: 115 FVIDQL 120
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 31.6 bits (72), Expect = 1.2
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAETELETILEDRAFKSRPTDGASVRDDTIRRDVSNER 63
EE K+ +L+EKI +L++ L ELE + E+ + + R +S R
Sbjct: 680 EELEEKIEELEEKIAELEKALAELRKELEELEEELE-------QLRKELEELSRQISALR 732
Score = 30.0 bits (68), Expect = 3.5
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAETELETILEDR 38
E KVAQL+ +I L ++ E LE LEDR
Sbjct: 382 ETLRSKVAQLELQIASLNNEIERLEARLE-RLEDR 415
>gnl|CDD|238327 cd00584, Prefoldin_alpha, Prefoldin alpha subunit; Prefoldin is a
hexameric molecular chaperone complex, found in both
eukaryotes and archaea, that binds and stabilizes newly
synthesized polypeptides allowing them to fold
correctly. The complex contains two alpha and four beta
subunits, the two subunits being evolutionarily related.
In archaea, there is usually only one gene for each
subunit while in eukaryotes there two or more paralogous
genes encoding each subunit adding heterogeneity to the
structure of the hexamer. The structure of the complex
consists of a double beta barrel assembly with six
protruding coiled-coils.
Length = 129
Score = 29.9 bits (68), Expect = 1.2
Identities = 10/40 (25%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 1 MDTEEAV----RKVAQLKEKIRQLKEDLTNAETELETILE 36
D EEA+ +K+ +L ++I +L+++L + ++ T+
Sbjct: 83 KDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEA 122
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 31.0 bits (71), Expect = 1.6
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 205 QPKVTSAKRFISAINRNTIVHAY 227
QP V K ++I +N + HAY
Sbjct: 11 QPVVV--KMLQNSIAKNRLSHAY 31
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 29.9 bits (68), Expect = 1.6
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 152 NASVLIVGCGGTGSPCIQYLAASGVGTLGLAD 183
VLI+G GG LA G + + +
Sbjct: 19 GKKVLILGAGGAARAVAYALAELGAAKIVIVN 50
>gnl|CDD|218434 pfam05103, DivIVA, DivIVA protein. The Bacillus subtilis divIVA1
mutation causes misplacement of the septum during cell
division, resulting in the formation of small,
circular, anucleate mini-cells. Inactivation of divIVA
produces a mini-cell phenotype, whereas overproduction
of DivIVA results in a filamentation phenotype. These
proteins appear to contain coiled-coils.
Length = 131
Score = 29.5 bits (67), Expect = 1.6
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 2 DTEEAVRKVAQLKEKIRQLKEDLTNAETELETI 34
D E ++ +LKE+I +L+E L + ET+
Sbjct: 33 DYEALYKENEELKEEIERLEEKLEEYKELEETL 65
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 30.4 bits (69), Expect = 2.2
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 3 TEEAVRKVAQLKEKIRQLKEDLTNAETELETILEDRAFKSRPTDGASVRDDTIRRD 58
E+ ++ +LK + Q + DL++A +LE K R + ++D+ R
Sbjct: 87 IEQKRERIEELKRALAQRRSDLSSASYQLE--------KRRASQLEKLQDEIKRTR 134
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 30.6 bits (70), Expect = 2.3
Identities = 34/138 (24%), Positives = 50/138 (36%), Gaps = 39/138 (28%)
Query: 406 DYRDEFLARRVAHTLLDVRSVDEFAM----MSLNI-------------------ASHATM 442
D+R FL L+DVRS EFA ++N+ A
Sbjct: 7 DFRALFLND---TPLIDVRSPIEFAEGHIPGAINLPLLNDEERAEVGTCYKQQGQFAAIA 63
Query: 443 ADVQLMFAEAGECPAFLES-LREDILAHRHVFVICRRGND-SQKVVQLLKRYVERHRPGV 500
L+ AG A E + A+ + C RG S V Q LK G
Sbjct: 64 LGHALV---AGNIAAHREEAWADFPRANPRGLLYCWRGGLRSGSVQQWLKEA------G- 113
Query: 501 VYDIRNIKEGYKGWQKYV 518
D+ ++ GYK ++++V
Sbjct: 114 -IDVPRLEGGYKAYRRFV 130
>gnl|CDD|140272 PTZ00245, PTZ00245, ubiquitin activating enzyme; Provisional.
Length = 287
Score = 30.4 bits (68), Expect = 2.4
Identities = 31/108 (28%), Positives = 49/108 (45%), Gaps = 9/108 (8%)
Query: 132 RYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSN 191
RY RQI L G Q++L++ SV + G G + + L +GV + +AD V ++
Sbjct: 8 RYDRQIRL--WGKSTQQQLMHTSVALHGVAGAAAEAAKNLVLAGVRAVAVADEGLVTDAD 65
Query: 192 LHRQVIHTTHTIGQPKVTSAKRFISAINR-NTIVHAYQ--TLLDTSNA 236
+ + G+ T R + A+ R N V Y T LD S+
Sbjct: 66 VCTNYLMQ----GEAGGTRGARALGALQRLNPHVSVYDAVTKLDGSSG 109
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 30.4 bits (69), Expect = 2.8
Identities = 7/36 (19%), Positives = 22/36 (61%)
Query: 2 DTEEAVRKVAQLKEKIRQLKEDLTNAETELETILED 37
+ E+ ++ +L+E + L++++ N ++EL+ +
Sbjct: 731 EEEKLKERLEELEEDLSSLEQEIENVKSELKELEAR 766
Score = 30.4 bits (69), Expect = 3.1
Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 10/90 (11%)
Query: 2 DTEEAVRKVAQLKEKIRQLKEDLTNAETELETI------LEDR-AFKSRPTDGASVRDDT 54
+ E+ ++ + + K+ QL DL+ E EL + +E + R A +
Sbjct: 442 EKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQRELAEAEAQARA 501
Query: 55 IRRDVSNERDTN---GAGQRGAHSTDSQVG 81
V R A +G H T +Q+G
Sbjct: 502 SEERVRGGRAVEEVLKASIQGVHGTVAQLG 531
>gnl|CDD|218483 pfam05183, RdRP, RNA dependent RNA polymerase. This family of
proteins are eukaryotic RNA dependent RNA polymerases.
These proteins are involved in post transcriptional gene
silencing where they are thought to amplify dsRNA
templates.
Length = 508
Score = 30.2 bits (68), Expect = 3.1
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 168 IQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTIGQPKVTSAKRFISAINRNTIVHAY 227
L + V +L + + + L+RQ+I T+G P + FI + +
Sbjct: 203 FDLLGDAAVNSLEIIRSSKPTPAYLNRQLITVLSTLGVPD----EVFIELLRE-ALKELA 257
Query: 228 QTLLDTSNACDIIRRY 243
+ L D A D++R+
Sbjct: 258 EALTDWDQALDLLRKQ 273
>gnl|CDD|236887 PRK11259, solA, N-methyltryptophan oxidase; Provisional.
Length = 376
Score = 29.8 bits (68), Expect = 3.2
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 155 VLIVGCGGTGSPCIQYLAASGVGTLGL 181
V+++G G GS YLA G+ LGL
Sbjct: 6 VIVIGLGSMGSAAGYYLARRGLRVLGL 32
>gnl|CDD|224550 COG1635, THI4, Ribulose 1,5-bisphosphate synthetase, converts PRPP
to RuBP, flavoprotein [Carbohydrate transport and
metabolism].
Length = 262
Score = 29.6 bits (67), Expect = 3.6
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 10/57 (17%)
Query: 123 SKFSKDITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGVGTL 179
K ++ ITERY +L L + V+IVG G +G YLA +G+
Sbjct: 11 VKITRAITERYFEDLL----------DYLESDVIIVGAGPSGLTAAYYLAKAGLKVA 57
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 29.2 bits (66), Expect = 3.9
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 8 RKVAQLKEKIRQLKEDLTNAETELETI 34
KV +L+E++ + + L A E I
Sbjct: 145 AKVEELEEELEEAESALEEARKRYEEI 171
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 29.8 bits (68), Expect = 4.1
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 148 EKLLNASVLIVGCGGTGSPCIQYLAASGVGTLGLA--DYDRVE 188
L VL++G G G ++LA GV + +A +R E
Sbjct: 178 GDLSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAE 220
>gnl|CDD|238791 cd01533, 4RHOD_Repeat_2, Member of the Rhodanese Homology Domain
superfamily, repeat 2. This CD includes putative
rhodanese-related sulfurtransferases which contain 4
copies of the Rhodanese Homology Domain. This CD aligns
the 2nd repeat which does contain the putative catalytic
Cys residue.
Length = 109
Score = 28.2 bits (63), Expect = 4.6
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 399 TEHLTALDYRDEFLARRVAHTLLDVRSVDEFAMMSLNIASHATMADVQLMFAEAGECPA 457
T ++A D AR +LD R DE+ M++ + A++ L E P
Sbjct: 9 TPSVSA-DELAALQARGAPLVVLDGRRFDEYRKMTIPGSVSCPGAELVLRVGELAPDPR 66
>gnl|CDD|203446 pfam06428, Sec2p, GDP/GTP exchange factor Sec2p. In
Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange
factor for Sec4p, which is required for vesicular
transport at the post-Golgi stage of yeast secretion.
Length = 90
Score = 27.7 bits (62), Expect = 5.0
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAETELET 33
+A R+ ++ K +L+E L ET L++
Sbjct: 40 ADARREREAVEIKNEKLEEQLKEKETLLDS 69
>gnl|CDD|167786 PRK04308, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 445
Score = 29.5 bits (66), Expect = 5.1
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 152 NASVLIVGCGGTGSPCIQYLAASGVGTLGLAD 183
N +L+ G GGTG I YL +G + D
Sbjct: 5 NKKILVAGLGGTGISMIAYLRKNG-AEVAAYD 35
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 29.8 bits (67), Expect = 5.2
Identities = 15/61 (24%), Positives = 25/61 (40%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAETELETILEDRAFKSRPTDGASVRDDTIRRDVSNER 63
E AVR++ + + + AE++ ED A + AS+R T+ V
Sbjct: 864 EVAVRELRHAATRAAEQRARAARAESDAREAAEDAAEARAEAEEASLRLRTLEESVGAMV 923
Query: 64 D 64
D
Sbjct: 924 D 924
>gnl|CDD|235234 PRK04164, PRK04164, hypothetical protein; Provisional.
Length = 181
Score = 28.6 bits (65), Expect = 5.4
Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 10/53 (18%)
Query: 472 VFVICRRGNDSQKVVQLLKRYVERHRPG---VVYDIRNIKEGYKGWQKYVDNR 521
+F++ +R +++++++K P + Y+ R+ K G+ W K V R
Sbjct: 132 LFILTKR-KREKELLEIIKEL----DPKAFIISYEPRSFKGGF--WTKGVRKR 177
>gnl|CDD|145231 pfam01946, Thi4, Thi4 family. This family includes a putative
thiamine biosynthetic enzyme.
Length = 229
Score = 29.0 bits (65), Expect = 5.6
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 10/51 (19%)
Query: 126 SKDITERYSRQILLDQVGVMGQEKLLNASVLIVGCGGTGSPCIQYLAASGV 176
S+ ITERY +L + V+IVG G +G YLA G+
Sbjct: 1 SRAITERYFEDLL----------DYAESDVVIVGAGPSGLTAAYYLAKKGL 41
>gnl|CDD|219890 pfam08537, NBP1, Fungal Nap binding protein NBP1. NBP1 is a
nuclear protein which has been shown in Saccharomyces
cerevisiae to be essential for the G2/M transition of
the cell cycle.
Length = 313
Score = 29.1 bits (65), Expect = 5.7
Identities = 16/61 (26%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 8 RKVAQLKEKIRQLKEDLTNAETELETILEDRAFKSRPTDGASVRDDTI--RRDVSNERDT 65
+K+ +L+EK+ +L+++L + + +L+ + E D A++ D+ + RRD+ N ++
Sbjct: 173 KKIDKLEEKLAELEQELQSTQKKLQFVKEKNHLLESLLDDANIDDEYVKSRRDIKNLQND 232
Query: 66 N 66
N
Sbjct: 233 N 233
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 29.3 bits (66), Expect = 5.7
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 153 ASVLIVGCGGTGSPCIQYLAASGVGTLGLADYDRVELSNLHRQVIHTTHTI 203
+V ++G GG GS IQ A G + D +L+ + + THT+
Sbjct: 189 ETVAVIGVGGVGSSAIQLAKAFGASPIIAVDVRDEKLAKA--KELGATHTV 237
>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein.
Length = 122
Score = 28.0 bits (63), Expect = 6.0
Identities = 8/40 (20%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAETELETI--LEDRAFK 41
+ +++ Q ++++ Q +E A E + + L +R K
Sbjct: 62 AQQQQELEQAEKQVEQAREQWQEANQERKKLEKLLEREKK 101
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 28.7 bits (65), Expect = 6.7
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 151 LNASVLIVGCGGTGSPCIQYLAASGVGTLGLADYD 185
L +V+++G G G IQ+L G + D D
Sbjct: 159 LGDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDID 193
>gnl|CDD|99813 cd06217, FNR_iron_sulfur_binding_3, Iron-sulfur binding ferredoxin
reductase (FNR) proteins combine the FAD and NAD(P)
binding regions of FNR with an iron-sulfur binding
cluster domain. Ferredoxin-NADP+ (oxido)reductase is an
FAD-containing enzyme that catalyzes the reversible
electron transfer between NADP(H) and electron carrier
proteins such as ferredoxin and flavodoxin. Isoforms of
these flavoproteins (i.e. having a non-covalently bound
FAD as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
between the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 235
Score = 28.8 bits (65), Expect = 6.8
Identities = 19/87 (21%), Positives = 27/87 (31%), Gaps = 17/87 (19%)
Query: 155 VLIVGCGGTG-SPC---IQYLAASG--------VGTLGLAD-YDRVELSNLHRQ--VIHT 199
VL+ GG+G P I+Y G D R EL L R+ +H
Sbjct: 111 VLL--AGGSGIVPLMSMIRYRRDLGWPVPFRLLYSARTAEDVIFRDELEQLARRHPNLHV 168
Query: 200 THTIGQPKVTSAKRFISAINRNTIVHA 226
T + + I + I
Sbjct: 169 TEALTRAAPADWLGPAGRITADLIAEL 195
>gnl|CDD|233811 TIGR02289, M3_not_pepF, oligoendopeptidase, M3 family. This
family consists of probable oligoendopeptidases in the
M3 family, related to lactococcal PepF and group B
streptococcal PepB (TIGR00181) but in a distinct clade
with considerable sequence differences. The likely
substrate is small peptides and not whole proteins, as
with PepF, but members are not characterized and the
activity profile may differ. Several bacteria have both
a member of this family and a member of the PepF
family.
Length = 549
Score = 29.0 bits (65), Expect = 7.2
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 10 VAQLKEKIRQLKEDLTNAETELETILED 37
+ +L++K +L E N++ E E + +
Sbjct: 1 IEELEKKFTELLEKFINSKEEQENWINE 28
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 28.5 bits (64), Expect = 7.3
Identities = 9/39 (23%), Positives = 24/39 (61%), Gaps = 3/39 (7%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAE---TELETILEDRA 39
+E +++ Q K +I++L++++ + E + +L+ RA
Sbjct: 69 DELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRA 107
>gnl|CDD|222808 PHA00666, PHA00666, putative protease.
Length = 233
Score = 28.5 bits (63), Expect = 7.3
Identities = 21/83 (25%), Positives = 27/83 (32%), Gaps = 18/83 (21%)
Query: 32 ETILEDRAFKSRPTDGASVRDDTIRRDVSNERDTNGAGQRGAHSTDSQVGDPASPEEIHR 91
E +L R +P DG S + GAG A GDP E
Sbjct: 5 ERLLMRRLCNEQPGDGGSQP--------AASEPAAGAGDNPA-----PQGDPTQEEGDKP 51
Query: 92 EPNNVNQTTESDNPNGPVKVEDD 114
+P +D P G K + D
Sbjct: 52 QP-----AAGADKPEGDKKADGD 69
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified as a putative NAD-dependent
epimerase/dehydratase. Atypical SDRs are distinct from
classical SDRs. Members of this subgroup have a
glycine-rich NAD(P)-binding motif that is related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site motif. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 251
Score = 28.4 bits (64), Expect = 7.5
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 155 VLIVGCGGTGSPCIQYLAASGVGTLGLA 182
VLI+GCG G + L A G G
Sbjct: 1 VLILGCGYLGQRLARQLLAQGWQVTGTT 28
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit
4. Members of this family function as part of the
Mediator (Med) complex, which links DNA-bound
transcriptional regulators and the general
transcription machinery, particularly the RNA
polymerase II enzyme. They play a role in basal
transcription by mediating activation or repression
according to the specific complement of transcriptional
regulators bound to the promoter.
Length = 176
Score = 28.1 bits (63), Expect = 7.6
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 8 RKVAQLKEKIRQLKEDLTNAETELETILEDRAFKSRPTDGASVRD 52
+V L EKI+ + ++L AE EL T+ + + S +
Sbjct: 36 AEVESLDEKIKDILKELKEAEKELRTLPDLSSINKANKRKVSSEE 80
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 28.4 bits (64), Expect = 7.8
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 154 SVLIVGCGGTGSPCIQYLAASG 175
+VL++G GG G Q A+G
Sbjct: 137 TVLVLGAGGVGLLAAQLAKAAG 158
>gnl|CDD|133477 cd06971, PgpA, Phosphatidylglycerophosphatase A; a bacterial
membrane-associated enzyme involved in lipid metabolism.
Phosphatidylglycerophosphatase A domain represents a
family of bacterial membrane-associated enzymes involved
in lipid metabolism. The prototype of this CD is a
putative Phosphatidylglycerophosphatase A (PGPase A)
from Listeria monocytogenes. PGPase A (EC: 3.1.3.27),
encoded by the gene pgpA, specifically catalyzes the
formation of phosphatidylglycerol from phosphatidyl
glycerophosphate (PGP). It requires Mg2+ for activity
and is inhibited by sulfhydryl agents and
freezing/thawing. PGPase B encoded from pgpB is not
included in this family, which also acts on phosphatidic
acid (PA) and lysophosphatidic acid (LPA). Aside from
PGPase A and B, evidence shows that there is another
PGPase existing in E. coli. Thus, PGPase A is not
essential for PGPase activity in E. coli.
Length = 143
Score = 27.9 bits (63), Expect = 8.4
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 303 AETVGTCGDNGVLGPVPGVMGTLQAVETIKLLIGLP 338
A + T +G+ PG G+L A+ LL L
Sbjct: 1 AHFLATGFGSGLSPIAPGTFGSLAALPLELLLSELG 36
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 28.7 bits (65), Expect = 8.6
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 2 DTEEAVRKVAQLKEKIRQLKEDLTNAETELETIL 35
D EE + +V +LKEK+++L+ L E EL+T+L
Sbjct: 69 DAEELIAEVKELKEKLKELEAALDELEAELDTLL 102
>gnl|CDD|218859 pfam06025, DUF913, Domain of Unknown Function (DUF913). Members of
this family are found in various ubiquitin protein
ligases.
Length = 359
Score = 28.5 bits (64), Expect = 8.6
Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 10/55 (18%)
Query: 450 AEAGECPAFLESLREDILAHRHVF--------VIC--RRGNDSQKVVQLLKRYVE 494
EAG AFL+++ ILA IC G K L+R +
Sbjct: 145 HEAGLSDAFLDAITPGILASSEAISCIPSAFGAICLNSSGLQLFKSKNALERLFK 199
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.9 bits (65), Expect = 8.7
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 1 MDTEEAVRKVAQLKEKIRQLKEDLTNAETELETILEDR 38
EE R++A L+E++ QL+ L E ELE + E+
Sbjct: 716 RQLEELKRELAALEEELEQLQSRLEELEEELEELEEEL 753
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 28.5 bits (64), Expect = 8.9
Identities = 12/41 (29%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 5 EAVRKVAQLKEKIRQLKEDLTN---AETELETILEDRAFKS 42
+ K+ ++K+++++LKE+LT A LE L+D+
Sbjct: 66 QKKDKIEEIKKELKELKEELTELSAALKALEAELQDKLLSI 106
>gnl|CDD|217281 pfam02910, Succ_DH_flav_C, Fumarate reductase flavoprotein
C-term. This family contains fumarate reductases,
succinate dehydrogenases and L-aspartate oxidases.
Length = 127
Score = 27.6 bits (62), Expect = 9.3
Identities = 11/39 (28%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 4 EEAVRKVAQLKEKIRQLKEDLTNAE--TELETILEDRAF 40
EEA+ K+ +L+E+ + ++ D + T+L LE
Sbjct: 22 EEALEKIKELRERFKNVRVDDKSKVFNTDLIEALELGNL 60
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.399
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,736,760
Number of extensions: 2625081
Number of successful extensions: 3384
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3316
Number of HSP's successfully gapped: 125
Length of query: 525
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 424
Effective length of database: 6,457,848
Effective search space: 2738127552
Effective search space used: 2738127552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.4 bits)